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comparison galaxy_stubs/BondOrderAssigner.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Preparation]-->
4 <tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0">
5 <description>computes bond order assignments for a ligand </description>
6 <macros>
7 <token name="@EXECUTABLE@">BondOrderAssigner</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>BondOrderAssigner
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_o:
18 -o $param_o
19 #end if
20 #if $param_max_sol:
21 -max_sol $param_max_sol
22 #end if
23 #if $param_scr_pen:
24 -scr_pen
25 #if " " in str($param_scr_pen):
26 "$param_scr_pen"
27 #else
28 $param_scr_pen
29 #end if
30 #end if
31 #if $param_non_opt:
32 -non_opt $param_non_opt
33 #end if
34 #if $adv_opts.adv_opts_selector=='advanced':
35 #if $adv_opts.param_o_id:
36 -o_id "$adv_opts.param_o_id"
37 #end if
38 #if $adv_opts.param_o_dir:
39 -o_dir "$adv_opts.param_o_dir"
40 #end if
41 #end if
42 </command>
43 <inputs>
44 <param name="param_i" type="data" format="mol2" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input mol2-file" help="(-i) "/>
45 <param name="param_max_sol" type="integer" min="0" max="100" optional="True" value="25" label="maximal number of assignments solutions to compute" help="(-max_sol) "/>
46 <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) ">
47 <option value="Antechamber">Antechamber</option>
48 <option value=" BALL"> BALL</option>
49 </param>
50 <param name="param_non_opt" type="integer" min="0" max="1" optional="True" value="0" label="compute sub-optimal assignments as well" help="(-non_opt) "/>
51 <expand macro="advanced_options">
52 <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) ">
53 <sanitizer>
54 <valid initial="string.printable">
55 <remove value="'"/>
56 <remove value="&quot;"/>
57 </valid>
58 </sanitizer>
59 </param>
60 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
61 <sanitizer>
62 <valid initial="string.printable">
63 <remove value="'"/>
64 <remove value="&quot;"/>
65 </valid>
66 </sanitizer>
67 </param>
68 </expand>
69 </inputs>
70 <outputs>
71 <data name="param_o" format="mol2"/>
72 </outputs>
73 <help>This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format.
74
75 Optional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt').
76
77 Output of this tool is a number of mol2 files each containing one bond order assignment.
78
79 To upload an input file please use the upload tool (Get Data -&gt; Upload File).
80
81 **Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help.
82
83 Please cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. &amp; Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011
84
85 </help>
86 </tool>